The final hurdle to allow the dumping of millions of tonnes of dredging spoil in the Great Barrier Reef's waters has been cleared after the Authority overseeing the marine park gave its approval, subject to environmental conditions.

The North Queensland Bulk Ports Corporation had applied to dredge and dump 3 million cubic metres of spoil in the reef waters as part of coal terminal expansion plans at Abbot Point, north of Bowen.

The plan has already been approved by federal Environment Minister Greg Hunt, with some environmental conditions, but the Great Barrier Reef Marine Park Authority had the final say over whether the dredge spoil could be dumped in the marine park that protects the reef.

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Dumping the spoil in the marine park was the only option put forward by the project proponents. Environmentalists have questioned why an onshore option was not considered.

Authority chairman Dr Russell Reichelt announced on Friday afternoon the body had given the go ahead subject to its own environmental conditions.

Dr Reichelt acknowledged there had been significant community debate and concern about the proposal, but added the decision was in line with the Authority's view that development on the reef should be kept to existing industrial areas.

“As a deepwater port that has been in operation for nearly 30 years, Abbot Point is better placed than other ports along the Great Barrier Reef coastline to undertake expansion as the capital and maintenance dredging required will be significantly less than what would be required in other areas," Dr Reichelt said.

“It's important to note the seafloor of the approved disposal area consists of sand, silt and clay and does not contain coral reefs or seagrass beds.”

The Authority placed 47 environmental conditions on the project, which they said included measures to reduce the impact on biodiversity including coral, long-term water quality monitoring and offset measures for commercial fishermen if the dumping caused other problems.

The dump site approved is 25 kilometres east-north-east of the Abbot Point port. As part of his approval, Mr Hunt has also required the proponents to investigate an alternative site 20 to 30 kilometres from the area being dredged.

Environment groups reacted swiftly to the decision, with World Wildlife Fund campaigner Richard Leck accusing the Authority and Mr Hunt of letting down the reef.

“This is a sad day for the reef and anyone who cares about its future,” he said.

Comment is being sought from the Bulk Ports Authority.

It comes as on Saturday the federal government will deliver to the World Heritage Committee a progress report on how it is meeting United Nations recommendations to protect the reef. The Committee has threatened to put the reef on a list of world heritage sites considered "in danger" unless sufficient progress is made on the recommendations.

In a report this week, the WWF and the Australian Marine Conservation Foundation argued the decision by Mr Hunt to allow the dredging and dumping had directly contravened a UN condition that no new development occur on the reef outside existing industrial areas.